Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-27

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All times shown according to UTC.

Time Nick Message
04:12 jbrefort joined #cdk
05:43 rojasm joined #cdk
06:02 CIA-31 blueobelisk: egonw * r121 /smiles-spec/ (. trunk/ trunk/smiles_spec.htm): Added location where the new SMILES-NG draft can go
06:03 CIA-31 blueobelisk: egonw * r122 /smiles-spec/trunk/ (smiles_spec.htm smiles_spec.html): Renamed, hoping that the SVN web interface will now spit it as text/html
06:05 CIA-31 blueobelisk: egonw * r123 /smiles-spec/trunk/smiles_spec.html: Set MIME via SVN prop
06:13 egonw joined #cdk
06:40 egonw rojasm: around?
06:40 rojasm hi, egonw
06:40 rojasm I received your email
06:41 rojasm I will try to find
06:41 rojasm it
06:41 egonw good
06:41 egonw maybe we can look at it together, so somewhere this afternoon or so?
06:41 rojasm ok
06:52 carsten joined #cdk
07:29 jpansanel moin
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09:23 CIA-31 bioclipse: ospjuth * r3849 /trunk/plugins/net.bioclipse/src/net/​bioclipse/BioclipseApplication.java: Renewed deprecated method calls
09:23 CIA-31 bioclipse: ospjuth * r3850 /trunk/plugins/net.bioclipse​/src/net/bioclipse/actions/ (AddExtensionsAction.java UpdateAction.java): Updated names of update actions
10:01 carsten joined #cdk
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11:31 CIA-31 bioclipse: ospjuth * r3851 /trunk/plugins/net.bioclipse/src/n​et/bioclipse/BioclipsePlugin.java: Stub to enable online update on startup. Not used yet as not restricted to bioclispe update sites only but contacts eclipse sites as well
11:31 CIA-31 bioclipse: ospjuth * r3852 /trunk/plugins/net.bioclipse/src/net/​bioclipse/actions/UpdateAction.java: Update action is restricted to only Bioclipse update sites
12:12 masak joined #cdk
13:03 CIA-31 bioclipse: jonalv * r3853 /trunk/playground/plugins/​net.bioclipse.structuredb/ (2 files in 2 dirs): Reworked the mapping structure. Realised that the Users password get's md5 encrypted one more time upon loading from database. Not good. Will have to change behavior of constructor or something...
13:23 CIA-31 bioclipse: jonalv * r3854 /trunk/playground/plugins/​net.bioclipse.structuredb/ (3 files in 3 dirs): All UserDao and LibraryDao tests except for update which I haven't started with yet now passes. As for Structure I am still not persisting the fingerprint and maybe some other stuff aswell.
13:31 CIA-31 jmol: hansonr * r8320 /trunk/Jmol/src/org/jmol/ (shape/Pmesh.java viewer/Eval.java viewer/Jmol.properties): 11.3.26 new feature: better reporting of PMESH file format errors
13:31 CIA-31 jmol: hansonr * r8321 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.26 version
13:33 CIA-31 jmol: hansonr * r8322 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.2.13 version
14:24 CIA-31 jmol: hansonr * r8323 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs): 11.3.26 -- version -- pmesh moved and privatized
14:33 CIA-31 jmol: hansonr * r8324 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): 11.3.26 code cleanup meshFileCollection moved to shapespecial
14:53 CIA-31 bioclipse: jonalv * r3855 /trunk/playground/plugins/​net.bioclipse.structuredb/ (5 files in 3 dirs): All dao tests pass for User and Library. Next thing is persisting all fields of a structure.
14:54 jonalv egonw, ping
14:57 egonw pong
14:57 jonalv egonw, I am going to persist smiles in a database
14:57 egonw OK, if you must
14:57 jonalv Can one say anythingabout the size of them?
14:58 egonw about linear with the number of atoms
14:58 egonw scaling factor of about 2?
14:58 jonalv right
14:58 jonalv Trying to figure out what datatype fits best
14:58 egonw string
14:58 jonalv yes but a very big one...
14:59 egonw yes
14:59 jonalv question is: how big?
14:59 egonw aim at small molecules... up to, say 300 atoms?
14:59 egonw (heavy atoms)
14:59 egonw so say, 5000 chars?
14:59 egonw to be on the safe side :)
15:00 jonalv so something like 5000 would be on the safe side?
15:01 jonalv I also wonder about fingerprints
15:01 jonalv The same thing actually...
15:01 egonw those tend to be fixed length
15:01 jonalv ah nice
15:01 egonw you might want to look at the SQL specs of the NMRShiftDB
15:01 jonalv do you have that number?
15:02 jonalv is that in CDK?
15:02 egonw no, sf.net/projects/nmrshiftdb
15:02 egonw not exactly sure where ...
15:02 egonw but somewhere in the repos
15:03 jonalv found the sourceforge page. Should be able to go on from there... thanks
15:06 jonalv hm they have used a medium blob for Smiles but they don't seem to have persisted the fingerprint...
15:07 CIA-31 blueobelisk: cjames53 * r124 /smiles-spec/trunk/ (25 files): Initial checkin of SMILES specification files.
15:07 egonw cool :)
15:07 egonw that was quick :)
15:07 CIA-31 jmol: hansonr * r8325 /trunk/Jmol/src/org/jmol/sh​apespecial/Isosurface.java: 11.3.26 isosurface code cleanup
15:07 egonw rojasm: around?
15:08 jonalv egonw, would fingerprint of a spectrum be the same as fingerprint of a molecule? Probably not eh?
15:08 egonw no, it would not :)
15:09 CIA-31 jmol: hansonr * r8326 /trunk/Jmol/src/org/jmol/shapespecial/Draw.java: 11.3.26 draw code cleanup
15:11 CIA-31 bioclipse: biocoder * r3856 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Worked on data sorting for plotting
15:12 CIA-31 jmol: hansonr * r8327 /trunk/Jmol/src/org/jmol/sha​pespecial/LcaoCartoon.java: 11.3.26 LcaoCartoon code cleanup
15:19 CIA-31 jmol: hansonr * r8328 /trunk/Jmol/src/org/jmol/shape​special/MolecularOrbital.java: 11.3.26 MolecularOrbital privitized
15:20 jonalv How big fingerprints are reasonable?
15:20 egonw dunno, see NMRShiftDB specs, or ask Stefan
15:21 jonalv k
15:28 CIA-31 jmol: hansonr * r8329 /trunk/Jmol/src/org/jmol/sh​apespecial/Polyhedra.java: 11.3.26 Polyhedra privitized
15:32 CIA-31 jmol: hansonr * r8330 /trunk/Jmol/src/org/jmol/shapes​pecial/PolyhedraRenderer.java: 11.3.26 PolyhedraRenderer privitized
15:35 rojasm left #cdk
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16:27 CIA-31 bioclipse: jonalv * r3857 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (3 files in 3 dirs):
16:27 CIA-31 bioclipse: Worked on persisting of structure. For the moment I solved the fingerprint
16:27 CIA-31 bioclipse: persisiting with a string of 1's and 0's this can be optimised later on. Had an
16:27 CIA-31 bioclipse: Eclipse-crash and now it complains about not finding a class. Not sure what
16:27 CIA-31 bioclipse: happend. Maybee it's only something on my computer but probably this commit will
16:27 CIA-31 bioclipse: contain the error...
16:46 CIA-31 jmol: hansonr * r8332 /trunk/Jmol/src/org/jmol/ (21 files in 4 dirs): 11.3.26 refactoring dipoles, geosurface, vectors into shapespecial
19:20 CIA-31 jmol: nicove * r8333 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
19:22 CIA-31 jmol: nicove * r8334 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
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20:47 CIA-31 cdk: rajarshi * r8976 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Added code for the 7th order chain case
22:32 CIA-31 jmol: hansonr * r8335 /branches/v11_2/Jmol/src/org/ (2 files in 2 dirs): 11.2.14 bug fix for application not accepting pastes into the console consisting of multiple lines
22:33 CIA-31 jmol: hansonr * r8336 /trunk/Jmol/src/org/ (2 files in 2 dirs): 11.3.27 bug fix for application not accepting pastes into the console consisting of multiple lines
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23:13 Bokoros http://tubeimage.com/viewer.php​?file=x7o3ydsiwmvc6pnvqyd3.jpg
23:14 Bokoros left #cdk

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